The present invention relates to a method of carrying out an amplification reaction and in particular a polymerase chain reaction (PCR) using an internal control mechanism.
Amplification reactions such as PCR reactions are well known and widely used. The PCR reaction procedure, in outline consists of the following steps, repeated cyclically.
Denaturation A mixture containing the PCR reagents (including the DNA to be copied, the individual nucleotide bases (A,T,G,C), suitable primers and polymerase enzyme) are heated to a predetermined temperature to separate the two strands of the target DNA.
Annealing: The mixture is then cooled to another predetermined temperature and the primers locate their complementary sequences on the DNA strands and bind to them.
Extension: The mixture is heated again to a further predetermined temperature. The polymerase enzyme (acting as a catalyst) joins the individual nucleotide bases to the end of the primer to form a new strand of DNA which is complementary to the sequence of the target DNA, the two strands being bound together.
A common problem in amplification reactions is establishing that the amplification has progressed adequately. In order to ensure that the amplification has progressed, it is common to include an xe2x80x9cinternal controlxe2x80x9d or standard sequence. This sequence is present in a known amount in the starting material and is designed such that it is amplified by the same primers as those used to amplify the target DNA sequence. The size of the amplified fragment however is different to that of the target DNA sequence. Hence, when the product is obtained, and analysed, for example using gel electrophoresis, the amplified control sequence produces a separate spot on the gel, and can indicate that the amplification reaction has progressed.
The problem with this method however is that because of the different size of the amplification target and the internal control sequence, they may be amplified with different efficiencies. Hence the degree of amplification of the control which has taken place will not be the same as that of the target sequence, which can give a misleading result in terms of the actual progress of the reaction.
The applicants have found an improved method for monitoring the progress of an amplification reaction, based upon the difference made to the hybridisation temperature of a sequence by the content of G and C bases present in the sequence.
The present invention provides a method for amplifying a target DNA sequence, said method comprising amplifying said sequence in the presence of (a) a nucleic acid polymerase (b) at least one primer capable of hybridising to said target polynucleotide, (c) a control sequence to which said primer is capable of hybridising and which is of similar length to the target DNA sequence but with a different percentage GC content, and (d) label means for detecting the hybridisation of nucleic acids in the reaction; and detecting the hybridisation of the target and control sequences at different temperatures.
Because the control sequence and the target sequence are of similar length, they will be amplified with similar amplification efficiencies. However, they will hybridise and denature at different temperatures, and so they will generate two discrete signals from the label means when they undergo denaturation in the course of the amplification reaction.
In general, the amplification will be effected in the presence of at least two primer sequences, a forward and reverse primer, which define each end of the sequences to be amplified, as is well known.
Suitable label means include are fluorescent labels. The signals can therefore be read using well known fluorescence monitoring devices.
Suitable fluorescent labels include intercalating dyes, which are interposed between the strands of a double stranded region of a DNA sequence. When the double stranded DNA region containing the intercalating dye reaches the predetermined temperature, it will be denatured, thus releasing the intercalating dye present between the strands. At this point the fluorescence from the mixture will reduce significantly, giving a readable signal.
The process using a double stranded DNA control sequence is illustrated diagrammatically in FIG. 1 hereinafter.
When intercalating dye (2) is added to a solution of double stranded DNA (1), it becomes interposed between the strands. The concentration of the dye (2) in this way produces a recognisable signal. On heating of the DNA so that it is denatured, dye is released and this event can be witnessed. Cooling to a temperature at which the said sequence will anneal again results in the intercalating dye becoming again trapped between the strands (see FIG. 1).
Suitable intercalating dyes include SYBRGreen(trademark), SYBRGold(trademark) and ethidium bromide or other commercially available dyes.
Alternatively, the fluorescent label used in the method of the invention may utilise fluorescence resonance transfer (FRET) as the basis of the signal. These labels utilise the transfer of energy between a reporter and a quencher molecule. The reporter molecule is excited with a specific wavelength of light for which it will normally exhibit a fluorescence emission wavelength. The quencher molecule is also excited at this wavelength such that it can accept the emission energy of the reporter molecule by resonance transfer when they are in close proximity (e.g. on the same, or a neighbouring molecule). The basis of FRET detection is to monitor the changes at reporter and quencher emission wavelengths.
For use in the context of the present invention, the control DNA sequence can be provided with a reporter and a quencher molecule, arranged so that the hybridisation of the strands alters the spatial relationship between the quencher and reporter molecules. Examples of such arrangements are illustrated in FIG. 2 and FIG. 3.
FIG. 2 illustrates an Example where the control sequence is a single stranded xe2x80x9chairpinxe2x80x9d type sequence (3), where the end portions hybridise together. A reporter molecule (4) is attached in the region of either the 5xe2x80x2 or the 3xe2x80x2 end of the sequence and a quencher molecule (5) is attached at the opposite end such that they are brought into close proximity when the sequence is in the form of the loop. In this arrangement, FRET occurs and so fluorescent signal from the reporter molecule is reduced whilst the signal from the quencher (5) molecule is enhanced.
On denaturation however, the opposed end regions of the sequence separate so that the reporter and quencher molecules become spaced and so FRET no longer occurs. This changes the signals from the respective molecules and so this event can be detected.
Another arrangement is illustrated in FIG. 3. In this case, the reporter (4) and quencher molecules (5) are located on different strands (6, 7 respectively) of a DNA control sequence and are located such that on hybridisation of the strands, they are brought into close proximity to each other so that FRET can occur.
Yet a further embodiment is illustrated in FIG. 4. In this case, an intercalating dye (2) is used as an element of the FRET system. A quencher molecule (5) which can absorb radiation from the dye may be arranged on a strand of the control sequence such that it can absorb radiation from dye which is close proximity to on hybridisation of the strands. When the control sequence reaches a temperature at which it is denatured, the dye (2) is dispersed and so the signal from the quencher molecule (5) changes.
This embodiment is advantageous in that only a single label need be applied to the control sequence. Single labelled sequences of this type are more economical to produce.
In yet a further embodiment (FIG. 5), the reporter (4) and quencher (5) molecules are positioned on two oligonucleotide strands (9 and 10 respectively) which do not hybridise together. They are however designed so that in use, they hydridise to a DNA sequence present in the reaction mixture, which may be a plasmid (11), such that the reporter (4) and quencher (5) are brought into close proximity and FRET can occur between them, giving a recognisable signal.
The DNA sequence to which they bind may be part of the reaction system, for example where the reaction being monitored is a PCR reaction wherein the DNA sequence comprises or is part of the amplification target sequence. Alternatively, the sequences may be added to the reaction in order to provide the basis for the temperature probe of the invention.
The control sequence of the invention may be designed so that it denatures at any desired predetermined temperature depending upon the amount of the bases G and C contained therein. It is known that the bases C and G bind together more strongly than A and T. Therefore, the greater the higher the content of the bases G and C contained within a sequence, the higher the melting point of the sequence will be. This feature is illustrated in FIG. 6 which shows the melting temperature of a DNA sequence plotted against the percentage of and GC base pairs which are present within in. Thus, by adjusting the GC content, the control sequence of a predetermined length may be designed so that it denatures at a temperature which is remote from that of the amplicon.
This facilitates the overcoming of another problem which is known to occur with amplification reactions which include conventional internal control sequences. Frequently, the copy number or concentration of the sequences present has a significant impact on the efficiency of the amplification. If one of either the target or the internal control sequence is present in high copy number or concentration, it will be amplified preferentially and the other will not be seen. Using internal controls of the invention, the amplification conditions, in particular the denaturing temperature, can be adjusted so as to limit amplification of the dominant amplicon so both signals can be detected.
For example, where one of the target sequence or the internal control is going to be present in higher quantities in the reaction, the internal control may be designed such that the denaturation temperature of the lower concentration component, for example the control, is lower than that of the high concentration sequence which in this case would be the target sequence. If then during the amplification reaction, the denaturation conditions are adjusted such that the higher denaturation temperature (of the target sequence for example) is not reached, the internal control only will be amplified, at least for a limited number of cycles, so as to generate a distinguishable signal.
Thus in a preferred embodiment, the amplification reaction is effected under conditions which favour the amplification of the one of the target sequence and under conditions which favour amplification of the internal control sequence. The denaturation temperature is the most convenient way of effecting this since by simply not allowing the mixture to reach the denaturation temperature of the higher melting component, the latter will not denature and so not hybridise with the primers and extend during the extension phase.
The method of the invention is particularly applicable for use in amplification reactions such as the polymerase chain reaction (PCR). In this case, the control sequence of the invention is introduced into the reaction vessel either separately to the target DNA sequence, or where appropriate, as part of the same plasmid.